Align Probable branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42 (uncharacterized)
to candidate WP_013537595.1 THEAM_RS04250 aminotransferase class IV
Query= curated2:P74921 (273 letters) >NCBI__GCF_000185805.1:WP_013537595.1 Length = 237 Score = 82.4 bits (202), Expect = 8e-21 Identities = 68/229 (29%), Positives = 100/229 (43%), Gaps = 6/229 (2%) Query: 32 ETLRTYSRAPFAAYKHYTRLKRSADFFNLPLSLSFDEFTKVLKAGADEFKQEVRIKVYLF 91 ET+R H+ R+ SA+ +LP +LSF+EF K +++ A VR + Sbjct: 8 ETVRVEKGRAVLLDYHFKRISSSAEALSLPFNLSFEEFGKAVESAATYDPALVR---FTL 64 Query: 92 PDSGEVLFVFSPLNIPDLETGVEVKISNVRRIPDLSTPPALKITGRTDIVLARREIVDCY 151 +SG L S I E + VR DLS + + L + Sbjct: 65 TESGYTLS--SRPCIKRQEAALMPFYGVVRVYSDLSLHKTVDVMSSL-YALKAAQSKGFD 121 Query: 152 DVILLGLNGQVCEGSFSNVFLVKEGKLITPSLDSGILDGITRENVIKLAKSLEIPVEERV 211 + +L G V E +F+N+F VK G L TPSL G L G R ++ LA+ + +PV E Sbjct: 122 EALLFDCRGFVSEAAFANLFFVKGGVLFTPSLKCGALPGTRRAFIVDLARQMGLPVVEGF 181 Query: 212 VWVWELFEADEMFLTHTSAGVVPVRRLNEHSFFEEEPGPVTATLMENFE 260 + L ADE+F+T PV R+ S E P+ + E E Sbjct: 182 FSLEGLLSADEVFITSAREDTCPVVRVGSFSLPRPEGKPLWLRIREAIE 230 Lambda K H 0.322 0.140 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 153 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 273 Length of database: 237 Length adjustment: 24 Effective length of query: 249 Effective length of database: 213 Effective search space: 53037 Effective search space used: 53037 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory